Mass Effect ROTS
by Watch Dogs
Summary: At the end of the suicide mission, Shepard is lost, or so everybody thinks. After being found and revived by the most unlikely allies, Shepard is placed in an old program that may turn the tide of the war. This is sligtly an AU.


Mass Effect: Return of a Spartan.

oOoOoOo

_Collector's base-2185CE_

_Fuck!_

Shepard wanted to smirk at how much he had screamed that in his head today but he didn't. Plasma pellets from the Collectors weapons pinged all around him as he made a left turn onto the last strip to the Normand SR2. He looked at Miranda. He had finally melted the ice she used to protect herself with and found the amazing woman behind it. He couldn't help it when his eyes wandered to her ass and he scolded himself.

_*Boom*_

Shepard dodged the grenade and stumbled a bit as he lost his footing. He felt Thane grab a hold of his shoulder pad and steady him on his foot once again. With a quick, thankful look he kept running when suddenly a pain erupted from his stomach. He looked down but his shields were intact and no bullet had touched him. The pain kept getting worse with every push to run faster and his vision doubled as the ground below him started shifting and moving. He could see Thane catching up with Miranda and they both jumped onto the Normandy as the ground started to move beneath him.

Shepard knew he had to move quickly so he pushed harder before reaching the end of the cliff and jumped for the Normandy. He was airborne for a few seconds and he really thought he might get on the ship but he started to fall and his stomach smashed against the deck which caused the pain to triple. His arms shot forward to grab onto anything he could and Miranda and Thane launched themselves at him. Both members of his crew grabbed onto any piece of his armour that they could and started to pull him into the Normandy.

"We have you John."

Gunfire kept pelting their position endlessly, Thane's shield snapped off and two bullets tore through his shoulder. He fell back, the Normandy's door opened and Joker came out with a gun in hand. As he fired, Grunt made his way out and helped in the efforts to pull up Shepard.

"You will not die yet young battle master."

Miranda nodded her face looked fierce yet slightly scared, "You promised John!"

Shepard nodded and smiled at Grunt as he slowly was pulled up onto the outside step of the Normandy's main door. He removed his helmet as he walked in but a thunderous explosion rocked the Normandy and the ship jolted back. Shepard's eyes grew wide as both people holding him up flew back and he fell down to the darkness below. He watched as Miranda stuck a hand out in desperation and tears fell from her eyes. A sad smile formed on his lips and he mouthed 'it'll be alright' to her. When he had first met her the thought of her crying would have made him laugh but now he never wanted to see her cry again. The ship began to grow smaller as he fell into the darkness and the battles noises grew faint. Shepard could see the damages as it flew off and felt relief as the crew flew out of the rubble into slip space.

_There safe... good..._

He looked to his left, reached out and grabbed his breather helmet before placing it back on. Shepard gasped in pain as his shoulder smashed into a rock on the way down and the pain spiked up through his body but he wasn't afraid to die. He had helped his team survive and helped Miranda become human again. He helped Samara square her daughter away, Jacob find his dad, and he kept Garrus from killing Sidonis. All his crew members had been helped and Shepard smiled knowing he had kept them from doing bad things. He closed his eyes as he smashed off a piece of debris which made him to do a slow flip. The pain in his stomach took his breath away again and blood poured out of his mouth and to spill onto the inside of his visor. His last coherent thought was of the best thing Miranda had ever graced him with... her smile.

-X-

Miranda sat on a small crate next to the door cargo door and tears streamed down her face. She felt lost. She had opened up to him, let him see the true her and look where it got her, sitting in the entrance dock crying. Miranda just wanted to have a life with him even if they had to fight through the Reapers to get it.

_But he broke his promise! ...he left me... _

Miranda flinched as the thunderous crack came from her right, through the door the closed, signalling Shepard's last gift to the galaxy returning to freedom... the Collector's base in ruins. She heard cheering, felt a hand on her shoulder and turned to see Garrus and Jack. Jack had an emotionless mask on it and Garrus seemed like he wanted to be sad. Despite his expression, he smiled at her in an attempt to keep her strong.

"You need to speak with the crew... they need to know."

Miranda didn't want to face them. It was bad enough they had seen, 'I'm in love' Miranda or what did Oriana say in the chat... 'Mirard or Mirishep'. She smiled at the stupid nicknames, gave a sniff and Jack handed her a Kleenex. Miranda eyed it curiously and was rewarded with Jack rolling her eyes.

"What? Think it's going to fucking bite you?"

Miranda smiled, "Thank you."

She blew her nose and gave her eyes a wipe before standing up. Jack smiled at her.

"Maybe you need to apply some make up... mascara running,"

Jack chuckled and Miranda could hear a little humour. She was never the best with jokes but she still smiled and walked with Jack. Miranda thought about telling Shepard that Jack was softening up but tears filled her eyes again as she reminded herself of what had happened. The PA system turned on and EDI started to speak.

"Attention all crew report to the conference room and take a seat or stand."

Miranda took a deep breath and walked down to Jokers seat and found him staring at his controls like they were evil. He raised his head and looked at Miranda.

"H…hi," Joker's voice didn't have its usual flare to it.

"Joker, are you coming with us?"

He looked at her, Garrus and Jack before but shook his head.

"I know what this is about; I don't need to relive it. It was my fault... I should have gone for him and took the risk."

A voice in the back of Miranda's head screamed for her to agree, to lash out but she ignored it.

"It's not your fault; Shep…he would have wanted you to save us all... stupid arse."

Joker smiled at her slightly and looked at the controls to the Normandy,

"I'm going to stay and talk with EDI... she's like a sister to me... a disembodied sister but a sister none the less."

Miranda nodded sympathizing with him as she knew what she would be doing tonight, crying to Oriana and looking for comfort. Miranda patted his shoulder, turned and made her way through CIC to the conference room. Her gait was slow and steady as she tried not to chicken out. She never used to feel this way. Miranda used to be cool, calm collected but now she had feelings and she didn't like them. When this had started she should have been able to go back to Cerberus without a second thought about Shepard but things had changed. He had gotten to her despite her best efforts. The door hissed as it opened and parted. The crew stood, there and looked at her with smiles which disappeared when Shepard didn't follow in after her.

"Ma'am, where is Commander Shepard?" asked Steven Albert a computer operator.

She looked at him and a frown twisted her expression.

"We... lost him."

Everybody's face instantly took a look of horror. Miranda almost felt satisfaction in the fact they were as miserable as her but she banished it. Rupert the cook pushed off the wall and glared at her.

"So what now,"

She knew he didn't like her but shrugged it off, "We go to the Alliance military... tell them what happened... we have no one else."

Some people nodded while others didn't do anything. The Illusive Man would kill them if they came near him after destroying the Collectors base.

"Everybody has the next week off."

Miranda left as EDI who had been listening in informed Joker of the new destination. Miranda got in the elevator, hit a button and before she realized it she was in Shepard's room. At first she felt like she should leave but she subconsciously got into his bed. It smelled like him. She buried her face into his pillow and slowly fell asleep.

-X-

_Reach-2185CE_

Lzarg walked down the metal hallway towards the observation room and he had no doubt that they had succeeded at their task. The place was deathly silent aside from a few beeps from doors telling that an alarm was ready to go off if they failed to input the right code. The Prothean walked up to the door and spoke in his language to open it.

"_The heroes of the past are the creations of blood and lies."_

The door opened up slowly and he found three other of his scientists inside. The last of the Protheans had become more of a researcher/scientific group and they had found thousands of things about the human past. When shields had first been used they were only used on ships until super soldiers had been made. Spartans. They had been the only group of people that could survive the still unstable Augmentations of their time. Spartans had been through two upgrades to the original Spartan program before the Covenant, a legendary race of aliens was removed. Spartan I hadn't worked and Spartan II and Spartan III had been the reasons the Covenant fell.

Reach, the main base for the Spartans was the ideal location for the Protheans to set up. It was deserted and destroyed so it offered a safe haven from any enemies. They took residence here and began researching the Spartans. The humans had disbanded the Spartans and Spartan 122; Steven Shepard had a son, John Shepard who had received his genes.

The old Augments were definitely stronger then the Augments the humans had currently but they were unstable to the point of human death. John Shepard could take the Augments because of his father's passed on genes and use them to easily win the war against the Reapers. The base they had chosen was known as Sword Base back when Reach was used as a military base. On the outside it looked broken, even destroyed but underneath was where the Prothean's began operating. The Prothean's had made sure to keep tabs on him and Lzarg looked into the med bay.

"_John Shepard_,"

Lzarg looked at the bloody man before him. They had already begun to inject him with medication but stopped when Shepard's heart monitor started to go off the charts and then his heart faltered. Lzarg panicked and hit a button to start the PA system in the med room.

"_Get him in a cryo pod"_

Two doctors brought him to one, across from where Lzarg was watching and placed him in before shutting the pod. Lzarg started examining him and gasped. They couldn't heal him. Something had screwed him up to the point where nothing they had could help him. His stomach and organs around it were rapidly eating themselves and it was spreading to his chest. The medicine that they had given him was being consumed by this super toxin and the medicine was the best they had to offer. Lzarg took a quick look through the pictures of Shepard's, insides taken by small bots placed in the medicine. He found a small circular object placed on one of his arteries, pumping in a black liquid. Lzarg's eyes narrowed as he caught a glimpse of the Cerberus logo.

"_Place a lock on the cryo pod_,"

He ordered the doctors; they nodded and did as told.

They would begin testing to find out how to save him. Until he could be saved he would take a back seat in this war... but what would be the consequences of his absence?

-X-

AN: How was it? Leave a review and tell me your thoughts, I really appreciate it. Yes this has a little bit of Halo in it but only a little. This will not be overly Halo'd up. As for Miranda's OOC-ness, this is after Shepard had gotten to her so she has more of her emotions showing. I am aware that the time and dates might be off between Halo and Mass Effect, but for the purpose of my story it doesn't matter. I'm also aware that the Protheans were supposed to have all died off but this story is AU. Also I'm not sure what the Collectors shoot so I assumed plasma pellets.

Thank you and any suggestions are welcomed, thanks.

Special Thanks:

-ttzdrkpl

-alimination602

-Sou7h

-Kaden-san


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